Thermal stability and hydration state of DNA G-quadruplex regulated by loop regions

Abstract

We designed and synthesized DNA oligonucleotides that were able to fold into intramolecular DNA G-quadruplexes with different number of G-quartet planes and thymines in the each loop region [GmTn: m indicates the number of G-quartet planes (2 <or= m <or= 4), and n indicates the number of thymines in the each loop region (2 <or= n <or= 4)]. Effects of molecular crowding on structure of G-quadruplexes were investigated by circular dichroism spectra in buffers containing 0 wt% or 40 wt% PEG200 (poly(ethylene glycol) with an average molecular weight of 200). The results showed that G2T2, G2T3, G2T4 and G3T4 folded into antiparallel G-quadruplexes under the dilute and molecular crowding conditions. On the other hand, G3T2, G3T3, G4T2, G4T3, and G4T4 underwent structural transitions from antiparallel or mixture to parallel G-quadruplex by the addition of PEG200. These result and thermodynamic analysis of G2Tn demonstrated that loop regions had pivotal roles to determine structure and stability of G-qudruplexes.